4DLC | Genus

Total Genus 90

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus	90
sequence length	280
structure length	222
Chain Sequence	VSLSPLILRSLAELQDGLNTVVDKNWRQLRRPGDWSLAITMEAAELLDSYPWKWWKNVKAQPDLQNVKIELTDILHFSLSGAMQVSDELADFMFFPLSDTNNALASFQNIIRLASLQRFQLVTSAVIAAADDIGFNLVAYYVAKHTLNGIRQMKGYKDGTYVKVQKGVEDNELLHGCISPFSLDDVTNEGNYKTKWDDIMHRVYDAFGTPKEERLNIGHWLK

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

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The Resolver thinks Pdb

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Time for openFile(/file/5d03ae02c73955f4e0c6bdc6/pdb.gz): 2339 ms

reading 222 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

222 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 48 ms

Adding embedded #jmolscript: select ({0:221});backbone only;select *;

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Hydrolase
source organism	Trypanosoma brucei
publication title	On the catalytic mechanism of dimeric dUTPases. pubmed doi rcsb
molecule keywords	Deoxyuridine triphosphatase
total genus	90
structure length	222
sequence length	280
ec nomenclature	ec 3.6.1.23: dUTP diphosphatase.
pdb deposition date	2012-02-06

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF08761	dUTPase_2	dUTPase

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
1.10.4010.10	Mainly Alpha	Orthogonal Bundle	all-alpha NTP pyrophosphatase fold	Type II deoxyuridine triphosphatase	4dlcA00

4DL8A 2CICA 4DLCA 4DK4A 4DKBA 1W2YA
chains in the Genus database with same CATH superfamily

4DL8A 2CICA 4DLCA 4DK4A 4DKBA 1W2YA
chains in the Genus database with same CATH topology

4DL8A 1OGLA 2CICA 2CJEA 2YB0A 4DK2A 2YAYA 4DLCA 1OGKA 4DK4A 2YAZA 4DKBA 1W2YA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 4DL8 A;  2CIC A;  4DLC A;  4DK4 A;  4DKB A;  1W2Y A; 
#chains in the Genus database with same CATH topology
 4DL8 A;  2CIC A;  4DLC A;  4DK4 A;  4DKB A;  1W2Y A; 
#chains in the Genus database with same CATH homology
 4DL8 A;  1OGL A;  2CIC A;  2CJE A;  2YB0 A;  4DK2 A;  2YAY A;  4DLC A;  1OGK A;  4DK4 A;  2YAZ A;  4DKB A;  1W2Y A;

...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

4DLCA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations